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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "scFastDE" in publications use:'
type: software
license: MIT
title: 'scFastDE: Fast Donor-Weighted Pseudo-Bulk Differential Expression for scRNA-seq'
version: 0.99.3
abstract: scFastDE provides fast, donor-weighted pseudo-bulk differential expression
  analysis for multi-donor single-cell RNA-seq experiments. Unlike existing tools
  that loop over genes serially, scFastDE uses vectorised sparse matrix operations
  across all genes simultaneously, achieving 10-50x speed gains on large datasets.
  Donors are weighted by the square root of their cell count, giving principled influence
  to well-represented donors without discarding donors with few cells. Paired experimental
  designs (same donors in multiple conditions) are automatically detected; pseudo-bulk
  is then aggregated per donor-condition pair and a blocking model accounts for inter-donor
  variation. A sparse pseudo-bulk guard automatically handles cell types where some
  donors fall below a minimum cell threshold. All functions operate natively on SingleCellExperiment
  objects.
authors:
- family-names: Jana
  given-names: Subhadip
  email: subhadipjana1409@gmail.com
  orcid: https://orcid.org/0009-0003-7860-2853
repository: https://bioc.r-universe.dev
repository-code: https://github.com/SubhadipJana1409/scFastDE
commit: 543071ed85a3d260095cf95942c55c4df5d8fcc8
url: https://github.com/SubhadipJana1409/scFastDE
date-released: '2026-06-04'
contact:
- family-names: Jana
  given-names: Subhadip
  email: subhadipjana1409@gmail.com
  orcid: https://orcid.org/0009-0003-7860-2853